166 research outputs found
Chemical potential in disordered organic materials
Charge carrier mobility in disordered organic materials is being actively
studied, motivated by several applications such as organic light emitting
diodes and organic field-effect transistors. It is known that the mobility in
disordered organic materials depends on the chemical potential which in turn
depends on the carrier concentration. However, the functional dependence of
chemical potential on the carrier concentration is not known. In this study, we
focus on the chemical potential in organic materials with Gaussian disorder. We
identify three cases of non-degenerate, degenerate and saturated regimes. In
each regime we calculate analytically the chemical potential as a function of
the carrier concentration and the energetic disorder from the first principles.Comment: 5 pages, 3 figure
Elastic response of filamentous networks with compliant crosslinks
Experiments have shown that elasticity of disordered filamentous networks
with compliant crosslinks is very different from networks with rigid
crosslinks. Here, we model and analyze filamentous networks as a collection of
randomly oriented rigid filaments connected to each other by flexible
crosslinks that are modeled as worm-like chains. For relatively large
extensions we allow for enthalpic stretching of crosslinks' backbones. We show
that for sufficiently high crosslink density, the network linear elastic
response is affine on the scale of the filaments' length. The nonlinear regime
can become highly nonaffine and is characterized by a divergence of the elastic
modulus at finite strain. In contrast to the prior predictions, we do not find
an asymptotic regime in which the differential elastic modulus scales linearly
with the stress, although an approximate linear dependence can be seen in a
transition from entropic to enthalpic regimes. We discuss our results in light
of the recent experiments.Comment: 10 pages, 11 figure
Active biopolymer networks generate scale-free but euclidean clusters
We report analytical and numerical modelling of active elastic networks,
motivated by experiments on crosslinked actin networks contracted by myosin
motors. Within a broad range of parameters, the motor-driven collapse of active
elastic networks leads to a critical state. We show that this state is
qualitatively different from that of the random percolation model.
Intriguingly, it possesses both euclidean and scale-free structure with Fisher
exponent smaller than . Remarkably, an indistinguishable Fisher exponent and
the same euclidean structure is obtained at the critical point of the random
percolation model after absorbing all enclaves into their surrounding clusters.
We propose that in the experiment the enclaves are absorbed due to steric
interactions of network elements. We model the network collapse, taking into
account the steric interactions. The model shows how the system robustly drives
itself towards the critical point of the random percolation model with absorbed
enclaves, in agreement with the experiment.Comment: 6 pages, 7 figure
Actively stressed marginal networks
We study the effects of motor-generated stresses in disordered three
dimensional fiber networks using a combination of a mean-field, effective
medium theory, scaling analysis and a computational model. We find that motor
activity controls the elasticity in an anomalous fashion close to the point of
marginal stability by coupling to critical network fluctuations. We also show
that motor stresses can stabilize initially floppy networks, extending the
range of critical behavior to a broad regime of network connectivities below
the marginal point. Away from this regime, or at high stress, motors give rise
to a linear increase in stiffness with stress. Finally, we demonstrate that our
results are captured by a simple, constitutive scaling relation highlighting
the important role of non-affine strain fluctuations as a susceptibility to
motor stress.Comment: 8 pages, 4 figure
How the DNA sequence affects the Hill curve of transcriptional response
The Hill coefficient is often used as a direct measure of the cooperativity
of binding processes. It is an essential tool for probing properties of
reactions in many biochemical systems. Here we analyze existing experimental
data and demonstrate that the Hill coefficient characterizing the binding of
transcription factors to their cognate sites can in fact be larger than one --
the standard indication of cooperativity -- even in the absence of any standard
cooperative binding mechanism. By studying the problem analytically, we
demonstrate that this effect occurs due to the disordered binding energy of the
transcription factor to the DNA molecule and the steric interactions between
the different copies of the transcription factor. We show that the enhanced
Hill coefficient implies a significant reduction in the number of copies of the
transcription factors which is needed to occupy a cognate site and, in many
cases, can explain existing estimates for numbers of the transcription factors
in cells. The mechanism is general and should be applicable to other biological
recognition processes.Comment: 9 pages, 7 figure
Classes of fast and specific search mechanisms for proteins on DNA
Problems of search and recognition appear over different scales in biological
systems. In this review we focus on the challenges posed by interactions
between proteins, in particular transcription factors, and DNA and possible
mechanisms which allow for a fast and selective target location. Initially we
argue that DNA-binding proteins can be classified, broadly, into three distinct
classes which we illustrate using experimental data. Each class calls for a
different search process and we discuss the possible application of different
search mechanisms proposed over the years to each class. The main thrust of
this review is a new mechanism which is based on barrier discrimination. We
introduce the model and analyze in detail its consequences. It is shown that
this mechanism applies to all classes of transcription factors and can lead to
a fast and specific search. Moreover, it is shown that the mechanism has
interesting transient features which allow for stability at the target despite
rapid binding and unbinding of the transcription factor from the target.Comment: 65 pages, 23 figure
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